Closed TamaraO closed 5 years ago
Dear Tamara,
I overlooked this thread, my apologies for that! The problem is actually hidden in the error message ("Genomes are not disjoint"). A genome is a set of reference sequences (e.g. chromosomes) with annotations (e.g., genes). If you supply two genomes, the reference sequences have to be disjoint (which makes e.g. sense for a host and virus genome). In your case, you must combine the the gtfs (cat
), and create a genome index for the human fasta and your combined gtf!
Best, Florian
Hi Florian,
I have two separate GTF files - one from GENCODE and another from de novo transcriptome assembly. I prepared indexes for both successfully. When I try to run start.bash script, it seems to run fine at first, but fails at MergeSams command:
What does the error
An error occurred: Genomes are not disjoint!
mean? How can I go about using two different references?Just in case, my
parameters.json
file looks like this:Thanks a lot!
Tamara